diff --git a/lightmotif-py/README.md b/lightmotif-py/README.md index b7719d5e95401aa978340c1c5616a55c5d3f8bfb..cb6e50c909364f3d959114930bcc3741f6d47fd7 100644 --- a/lightmotif-py/README.md +++ b/lightmotif-py/README.md @@ -5,7 +5,7 @@ [](https://github.com/althonos/lightmotif/actions) [](https://codecov.io/gh/althonos/lightmotif/) [](https://choosealicense.com/licenses/mit/) -[](https://lightmotif.readthedocs.io) +[](https://lightmotif.readthedocs.io/en/stable/) [](https://crates.io/crates/lightmotif-py) [](https://pypi.org/project/lightmotif) [](https://pypi.org/project/lightmotif/#files) diff --git a/lightmotif-py/docs/index.rst b/lightmotif-py/docs/index.rst index 757e8c7d8e8015cad3108647ae5ac4393fa14978..5c8a8e024838a786647f8c1216524b23ffd5a386 100644 --- a/lightmotif-py/docs/index.rst +++ b/lightmotif-py/docs/index.rst @@ -31,8 +31,8 @@ .. |License| image:: https://img.shields.io/badge/license-MIT-blue.svg?style=flat-square&maxAge=2678400 :target: https://choosealicense.com/licenses/mit/ -.. |Docs| image:: https://img.shields.io/readthedocs/lightmotif/latest?style=flat-square&maxAge=600 - :target: https://lightmotif.readthedocs.io +.. |Docs| image:: https://img.shields.io/readthedocs/lightmotif/stable?style=flat-square&maxAge=600 + :target: https://lightmotif.readthedocs.io/en/stable/ .. |Crate| image:: https://img.shields.io/crates/v/lightmotif-py.svg?maxAge=600&style=flat-square :target: https://crates.io/crates/lightmotif-py @@ -90,10 +90,29 @@ searches for a motif encoded in a position weight matrix. The position scanning combines several techniques to allow high-throughput processing of sequences: -- Compile-time definition of alphabets and matrix dimensions. -- Sequence symbol encoding for fast table look-ups, as implemented in HMMER or MEME -- Striped sequence matrices to process several positions in parallel, inspired by Michael Farrar. -- Vectorized matrix row look-up using ``permute`` instructions of `AVX2 <https://fr.wikipedia.org/wiki/Advanced_Vector_Extensions>`_. +.. grid:: 1 2 4 4 + :gutter: 1 + + .. grid-item-card:: :fas:`fa-solid fa-arrow-down-a-z` Constant alphabets + + Compile-time definition of alphabets and matrix dimensions, allowing + constant pointer incrementation in loops over strided arrays. + + .. grid-item-card:: :fas:`fa-solid fa-arrow-down-1-9` Ordinal encoding + + Sequence symbol encoding as indices fo fast table look-ups, as + implemented in `HMMER <https://hmmer.org>`_ or + `MEME <https://meme-suite.org/>`_. + + .. grid-item-card:: :fas:`fa-solid fa-table` Striped matrices + + Striped sequence matrices for parallel processing, + inspired by Michael Farrar (:pmid:`17110365`). + + .. grid-item-card:: :fas:`fa-solid fa-microchip` Platform code + + Vectorized matrix-row look-up using ``permute`` instructions of + `AVX2 <https://fr.wikipedia.org/wiki/Advanced_Vector_Extensions>`_. *This is the Python version, there is a* `Rust crate <https://docs.rs/lightmotif>`_ *available as well.*